
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms    8 (   32),  selected    8 , name T0372TS383_5-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS383_5-D1.T0372_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      I       2           -
LGA    -       -      P       3           -
LGA    -       -      F       4           -
LGA    -       -      K       5           -
LGA    -       -      D       6           -
LGA    -       -      I       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      A      10           -
LGA    -       -      D      11           -
LGA    -       -      R      12           -
LGA    -       -      D      13           -
LGA    -       -      T      14           -
LGA    -       -      I      15           -
LGA    -       -      T      16           -
LGA    -       -      A      17           -
LGA    -       -      F      18           -
LGA    -       -      T      19           -
LGA    -       -      M      20           -
LGA    -       -      K      21           -
LGA    -       -      S      22           -
LGA    -       -      D      23           -
LGA    -       -      R      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    -       -      S      30           -
LGA    -       -      F      31           -
LGA    -       -      S      32           -
LGA    -       -      N      33           -
LGA    -       -      L      34           -
LGA    -       -      C      35           -
LGA    -       -      S      36           -
LGA    -       -      W      37           -
LGA    -       -      R      38           -
LGA    -       -      F      39           -
LGA    -       -      L      40           -
LGA    -       -      Y      41           -
LGA    -       -      D      42           -
LGA    -       -      T      43           -
LGA    -       -      Q      44           -
LGA    -       -      F      45           -
LGA    -       -      A      46           -
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      D      49           -
LGA    -       -      D      50           -
LGA    -       -      F      51           -
LGA    -       -      L      52           -
LGA    -       -      V      53           -
LGA    -       -      F      54           -
LGA    -       -      K      55           -
LGA    -       -      F      56           -
LGA    -       -      W      57           -
LGA    -       -      A      58           -
LGA    -       -      G      59           -
LGA    -       -      E      60           -
LGA    -       -      Q      61           -
LGA    -       -      L      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    -       -      M      65           -
LGA    -       -      M      66           -
LGA    -       -      P      67           -
LGA    -       -      V      68           -
LGA    -       -      G      69           -
LGA    -       -      N      70           -
LGA    -       -      G      71           -
LGA    -       -      D      72           -
LGA    -       -      L      73           -
LGA    -       -      K      74           -
LGA    -       -      A      75           -
LGA    -       -      V      76           -
LGA    K     290      L      77          1.004
LGA    Y     291      R      78          2.661
LGA    M     292      K      79          1.230
LGA    C     294      L      80          3.073
LGA    -       -      I      81           -
LGA    -       -      E      82           -
LGA    L     295      D      83          2.006
LGA    K     296      A      84          2.379
LGA    -       -      D      85           -
LGA    -       -      K      86           -
LGA    -       -      E      87           -
LGA    -       -      K      88           -
LGA    -       -      H      89           -
LGA    D     297      N      90          2.597
LGA    H     298      F      91          1.443
LGA    -       -      C      92           -
LGA    -       -      M      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      V      96           -
LGA    -       -      C      97           -
LGA    -       -      S      98           -
LGA    -       -      N      99           -
LGA    -       -      M     100           -
LGA    -       -      R     101           -
LGA    -       -      A     102           -
LGA    -       -      D     103           -
LGA    -       -      L     104           -
LGA    -       -      E     105           -
LGA    -       -      A     106           -
LGA    -       -      I     107           -
LGA    -       -      L     108           -
LGA    -       -      P     109           -
LGA    -       -      E     110           -
LGA    -       -      R     111           -
LGA    -       -      F     112           -
LGA    -       -      I     113           -
LGA    -       -      F     114           -
LGA    -       -      T     115           -
LGA    -       -      E     116           -
LGA    -       -      D     117           -
LGA    -       -      K     290           -
LGA    -       -      Y     291           -
LGA    -       -      M     292           -
LGA    -       -      A     293           -
LGA    -       -      C     294           -
LGA    -       -      L     295           -
LGA    -       -      K     296           -
LGA    -       -      D     297           -
LGA    -       -      H     298           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    8  126    5.0      8    2.17     0.00      5.047     0.353

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.032164 * X  +  -0.179271 * Y  +  -0.983274 * Z  +  79.894699
  Y_new =   0.950218 * X  +  -0.299570 * Y  +   0.085700 * Z  +  62.735806
  Z_new =  -0.309923 * X  +  -0.937080 * Y  +   0.160712 * Z  +  58.626385 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.400946    1.740646  [ DEG:   -80.2683     99.7317 ]
  Theta =   0.315112    2.826481  [ DEG:    18.0546    161.9454 ]
  Phi   =   1.536960   -1.604632  [ DEG:    88.0613    -91.9387 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0372TS383_5-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS383_5-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    8  126   5.0    8   2.17    0.00   5.047
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS383_5-D1
PFRMAT TS
TARGET T0372
MODEL 5
PARENT 1yvoA
ATOM    529  N   LYS   290      32.133  58.816  -4.285  1.00  0.00
ATOM    530  CA  LYS   290      31.949  58.154  -5.586  1.00  0.00
ATOM    531  C   LYS   290      32.487  58.956  -6.788  1.00  0.00
ATOM    532  O   LYS   290      31.928  58.895  -7.894  1.00  0.00
ATOM    533  N   TYR   291      33.561  59.712  -6.564  1.00  0.00
ATOM    534  CA  TYR   291      34.151  60.526  -7.627  1.00  0.00
ATOM    535  C   TYR   291      35.056  59.709  -8.527  1.00  0.00
ATOM    536  O   TYR   291      35.432  60.159  -9.615  1.00  0.00
ATOM    537  N   MET   292      35.403  58.502  -8.082  1.00  0.00
ATOM    538  CA  MET   292      36.288  57.669  -8.886  1.00  0.00
ATOM    539  C   MET   292      35.832  56.234  -8.907  1.00  0.00
ATOM    540  O   MET   292      34.855  55.870  -8.248  1.00  0.00
ATOM    541  N   CYS   294      36.531  55.419  -9.681  1.00  0.00
ATOM    542  CA  CYS   294      36.223  53.998  -9.742  1.00  0.00
ATOM    543  C   CYS   294      37.510  53.195  -9.895  1.00  0.00
ATOM    544  O   CYS   294      38.468  53.654 -10.524  1.00  0.00
ATOM    545  N   LEU   295      37.531  52.003  -9.303  1.00  0.00
ATOM    546  CA  LEU   295      38.582  51.028  -9.570  1.00  0.00
ATOM    547  C   LEU   295      38.062  49.681  -9.130  1.00  0.00
ATOM    548  O   LEU   295      37.229  49.612  -8.225  1.00  0.00
ATOM    549  N   LYS   296      38.563  48.617  -9.760  1.00  0.00
ATOM    550  CA  LYS   296      38.155  47.243  -9.423  1.00  0.00
ATOM    551  C   LYS   296      36.644  47.034  -9.571  1.00  0.00
ATOM    552  O   LYS   296      36.057  46.197  -8.891  1.00  0.00
ATOM    553  N   ASP   297      36.017  47.777 -10.478  1.00  0.00
ATOM    554  CA  ASP   297      34.570  47.695 -10.679  1.00  0.00
ATOM    555  C   ASP   297      33.664  48.253  -9.580  1.00  0.00
ATOM    556  O   ASP   297      32.482  47.901  -9.509  1.00  0.00
ATOM    557  N   HIS   298      34.199  49.113  -8.712  1.00  0.00
ATOM    558  CA  HIS   298      33.373  49.774  -7.684  1.00  0.00
ATOM    559  C   HIS   298      33.657  51.273  -7.573  1.00  0.00
ATOM    560  O   HIS   298      34.767  51.699  -7.861  1.00  0.00
TER
END
